Bioconductor Centipede

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R centipede

updated 6.2 years ago by James W. MacDonald 63k • written 6.2 years ago by rbronste ▴ 60

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footprinting centipede atac-seq dnaseq

6.2 years ago rbronste ▴ 60

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Answer: Individual DESeq2 runs versus a single DESeq2 run with contrasts produce differe by ATpoint ★ 2.9k

Please see the vignette, spitting samples or keeping together is covered there. This was asked many times before, use google or the search …

Comment: Error in loadFUN(x, seqname, ranges) : trying to load regions beyond the boun by merve.sahn • 0

I guess you are mixing the NCBI and UCSC annotations. If you are using a custom-edited code to load the annotations, I would recommend clon…

Comment: HiCDCPlus extract_hic_eigenvectors() only works with larger bin sizes (> =250kb by merve.sahn • 0

Unfortunately, that seems to be your issue. There is a relevant thread [here](https://groups.google.com/g/3d-genomics/c/hVVTxXpPcxs?pli=1).

Comment: HiCDCPlus `construct_features` incompatible with BSgenome.Hsapiens.NCBI.T2T.CHM1 by merve.sahn • 0

Hi @Gemma-Zhang-326 , the package currently runs only on genomes and versions with UCSC annotations. I will need to issue an update to use …

Answer: Affymetrix analysis Chiptype hgu133plus2hsentrezg.db vs hgu133plus2.db by Guido Hooiveld ★ 3.6k

I am not familiar with Chipster, but `hgu133plus2hsentrezg.db` refers to the annotation of the Affymetrix HGU133plus2 GeneChip that is base…

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DESeq2 Error from Installing a Package

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